Controllable lossy compression of BAM/CRAM files
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
keepbed{:bash}
BED file defining regions to keep quality
bedout{:bash}
:boolean
set to true to output suspicious regions to a BED file
bam{:bash}
*.bam{:bash}
optional filtered/compressed BAM file
*.{bam}
cram{:bash}
*.cram{:bash}
optional filtered/compressed CRAM file
*.{cram}
sam{:bash}
*.sam{:bash}
optional filtered/compressed SAM file
*.{sam}
bed{:bash}
*.bed{:bash}
optional suspicious regions BED file
*{bed}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
